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- EMDB-45659: Particulate methane monooxygenase in washed native membranes -

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Basic information

Entry
Database: EMDB / ID: EMD-45659
TitleParticulate methane monooxygenase in washed native membranes
Map data
Sample
  • Organelle or cellular component: particulate methane monooxygenase in washed native membranes
    • Protein or peptide: Particulate methane monooxygenase gamma subunit
    • Protein or peptide: Particulate methane monooxygenase beta subunit
    • Protein or peptide: Particulate methane monooxygenase alpha subunit
  • Ligand: (2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexadecanoyloxy)propyl (9Z)-heptadec-9-enoate
  • Ligand: COPPER (II) ION
  • Ligand: water
Keywordsmembrane protein / metalloenzyme / monooxygenase / OXIDOREDUCTASE
Function / homology
Function and homology information


methane monooxygenase (particulate) / methane monooxygenase (soluble) / methane monooxygenase [NAD(P)H] activity / monooxygenase activity / metal ion binding / membrane
Similarity search - Function
Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal / Ammonia monooxygenase/particulate methane monooxygenase, subunit C domain superfamily / Ammonia/particulate methane monooxygenase, subunit A superfamily / Ammonia monooxygenase / Ammonia monooxygenase/methane monooxygenase, subunit C / Ammonia monooxygenase/particulate methane monooxygenase, subunit B / Ammonia/methane monooxygenase, subunitB, N-terminal / Monooxygenase subunit B protein
Similarity search - Domain/homology
Particulate methane monooxygenase alpha subunit / Ammonia monooxygenase/methane monooxygenase, subunit C family protein / Particulate methane monooxygenase beta subunit
Similarity search - Component
Biological speciesMethylococcus capsulatus str. Bath (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsTucci FJ / Rosenzweig AC
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118035 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM105538 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)F31ES034283 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structures of methane and ammonia monooxygenases in native membranes.
Authors: Frank J Tucci / Amy C Rosenzweig /
Abstract: Methane- and ammonia-oxidizing bacteria play key roles in the global carbon and nitrogen cycles, respectively. These bacteria use homologous copper membrane monooxygenases to accomplish the defining ...Methane- and ammonia-oxidizing bacteria play key roles in the global carbon and nitrogen cycles, respectively. These bacteria use homologous copper membrane monooxygenases to accomplish the defining chemical transformations of their metabolisms: the oxidations of methane to methanol by particulate methane monooxygenase (pMMO) and ammonia to hydroxylamine by ammonia monooxygenase (AMO), enzymes of prime interest for applications in mitigating climate change. However, investigations of these enzymes have been hindered by the need for disruptive detergent solubilization prior to structure determination, confounding studies of pMMO and precluding studies of AMO. Here, we overcome these challenges by using cryoEM to visualize pMMO and AMO directly in their native membrane arrays at 2.4 to 2.8 Å resolution. These structures reveal details of the copper centers, numerous bound lipids, and previously unobserved components, including identifiable and distinct supernumerary helices interacting with pMMO and AMO, suggesting a widespread role for these helices in copper membrane monooxygenases. Comparisons between these structures, their metallocofactors, and their unexpected protein-protein interactions highlight features that may govern activity or the formation of higher-order arrays in native membranes. The ability to obtain molecular insights within the native membrane will enable further understanding of these environmentally important enzymes.
History
DepositionJul 10, 2024-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45659.png

Downloads & links

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Map

FileDownload / File: emd_45659.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.46752632 - 0.8351151
Average (Standard dev.)0.0009871478 (±0.025591658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45659_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45659_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : particulate methane monooxygenase in washed native membranes

EntireName: particulate methane monooxygenase in washed native membranes
Components
  • Organelle or cellular component: particulate methane monooxygenase in washed native membranes
    • Protein or peptide: Particulate methane monooxygenase gamma subunit
    • Protein or peptide: Particulate methane monooxygenase beta subunit
    • Protein or peptide: Particulate methane monooxygenase alpha subunit
  • Ligand: (2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexadecanoyloxy)propyl (9Z)-heptadec-9-enoate
  • Ligand: COPPER (II) ION
  • Ligand: water

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Supramolecule #1: particulate methane monooxygenase in washed native membranes

SupramoleculeName: particulate methane monooxygenase in washed native membranes
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)

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Macromolecule #1: Particulate methane monooxygenase gamma subunit

MacromoleculeName: Particulate methane monooxygenase gamma subunit / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (soluble)
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)
Molecular weightTheoretical: 27.954148 KDa
SequenceString: EAPLLDKKWL TFALAIYTVF YLWVRWYEGV YGWSAGLDSF APEFETYWMN FLYTEIVLEI VTASILWGYL WKTRDRNLAA LTPREELRR NFTHLVWLVA YAWAIYWGAS YFTEQDGTWH QTIVRDTDFT PSHIIEFYLS YPIYIITGFA AFIYAKTRLP F FAKGISLP ...String:
EAPLLDKKWL TFALAIYTVF YLWVRWYEGV YGWSAGLDSF APEFETYWMN FLYTEIVLEI VTASILWGYL WKTRDRNLAA LTPREELRR NFTHLVWLVA YAWAIYWGAS YFTEQDGTWH QTIVRDTDFT PSHIIEFYLS YPIYIITGFA AFIYAKTRLP F FAKGISLP YLVLVVGPFM ILPNVGLNEW GHTFWFMEEL FVAPLHYGFV IFGWLALAVM GTLTQTFYSF AQGGLGQSLC E

UniProtKB: Ammonia monooxygenase/methane monooxygenase, subunit C family protein

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Macromolecule #2: Particulate methane monooxygenase beta subunit

MacromoleculeName: Particulate methane monooxygenase beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (particulate)
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)
Molecular weightTheoretical: 27.855434 KDa
SequenceString: SAVRSHAEAV QVSRTIDWMA LFVVFFVIVG SYHIHAMLTM GDWDFWSDWK DRRLWVTVTP IVLVTFPAAV QSYLWERYRL PWGATVCVL GLLLGEWINR YFNFWGWTYF PINFVFPASL VPGAIILDTV LMLSGSYLFT AIVGAMGWGL IFYPGNWPII A PLHVPVEY ...String:
SAVRSHAEAV QVSRTIDWMA LFVVFFVIVG SYHIHAMLTM GDWDFWSDWK DRRLWVTVTP IVLVTFPAAV QSYLWERYRL PWGATVCVL GLLLGEWINR YFNFWGWTYF PINFVFPASL VPGAIILDTV LMLSGSYLFT AIVGAMGWGL IFYPGNWPII A PLHVPVEY NGMLMSIADI QGYNYVRTGT PEYIRMVEKG TLRTFGKDVA PVSAFFSAFM SILIYFMWHF IGRWFSNERF LQ S

UniProtKB: Particulate methane monooxygenase beta subunit

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Macromolecule #3: Particulate methane monooxygenase alpha subunit

MacromoleculeName: Particulate methane monooxygenase alpha subunit / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)
Molecular weightTheoretical: 42.832887 KDa
SequenceString: HGEKSQAAFM RMRTIHWYDL SWSKEKVKIN ETVEIKGKFH VFEGWPETVD EPDVAFLNVG MPGPVFIRKE SYIGGQLVPR SVRLEIGKT YDFRVVLKAR RPGDWHVHTM MNVQGGGPII GPGKWITVEG SMSEFRNPVT TLTGQTVDLE NYNEGNTYFW H AFWFAIGV ...String:
HGEKSQAAFM RMRTIHWYDL SWSKEKVKIN ETVEIKGKFH VFEGWPETVD EPDVAFLNVG MPGPVFIRKE SYIGGQLVPR SVRLEIGKT YDFRVVLKAR RPGDWHVHTM MNVQGGGPII GPGKWITVEG SMSEFRNPVT TLTGQTVDLE NYNEGNTYFW H AFWFAIGV AWIGYWSRRP IFIPRLLMVD AGRADELVSA TDRKVAMGFL AATILIVVMA MSSANSKYPI TIPLQAGTMR GM KPLELPA PTVSVKVEDA TYRVPGRAMR MKLTITNHGN SPIRLGEFYT ASVRFLDSDV YKDTTGYPED LLAEDGLSVS DNS PLAPGE TRTVDVTASD AAWEVYRLSD IIYDPDSRFA GLLFFFDATG NRQVVQIDAP LIPSFM

UniProtKB: Particulate methane monooxygenase alpha subunit

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Macromolecule #4: (2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexadecan...

MacromoleculeName: (2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexadecanoyloxy)propyl (9Z)-heptadec-9-enoate
type: ligand / ID: 4 / Number of copies: 57 / Formula: A1A0P
Molecular weightTheoretical: 703.97 Da

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Macromolecule #5: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 5 / Number of copies: 9 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 573 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

BufferpH: 7.3
Sugar embeddingMaterial: vitreous ice
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7s4h

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129495
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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